A genome-wide DNA methylation signature for SETD1B-related syndrome

Krzyzewska, Izabela M.; Maas, Saskia M.; Henneman, Peter; Lip, Karin van der; Venema, Andrea; Barañano, Kristin W.; Chassevent, Anna; Aref‐Eshghi, Erfan; Essen, Anthonie J. van; Fukuda, Tokiko; Ikeda, Hiroko; Jacquemont, Marie Line; Kim, H.-G.; Labalme, Audrey; Sm, Lewis; Lesca, Gaëtan; Madrigal, Irene; Mahida, Sonal; Matsumoto, Naomichi; Rabionet, Raquel; Rajcan‐Separovic, Evica; Qiao, Ying; Sadiković, Bekim; Saitsu, Hirotomo; Sweetser, David A.; Alders, Mariëlle; Mannens, Marcel M.A.M.

doi:10.1186/s13148-019-0749-3

Cited by 51 publications

(56 citation statements)

References 32 publications

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“…In this region, we also identified SETD1B gene (Histone-lysine N-methyltransferase SETD1B, 53.06 Mb) which encodes a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 and is responsible for the epigenetic control of chromatin structure and gene expression. A specific hypermethylation signature was associated with loss of function mutations in the SETD1B gene ( Krzyzewska et al, 2019 ). The NCOA3 gene (nuclear receptor coactivator 3; OAR13: 32.0 Mb) encodes a nuclear receptor coactivator with histone acetyltransferase activity.…”

Section: Discussionmentioning

confidence: 99%

Genetic Determinism Exists for the Global DNA Methylation Rate in Sheep

et al. 2020

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Recent studies showed that epigenetic marks, including DNA methylation, influence production and adaptive traits in plants and animals. So far, most studies dealing with genetics and epigenetics considered DNA methylation sites independently. However, the genetic basis of the global DNA methylation rate (GDMR) remains unknown. The main objective of the present study was to investigate genetic determinism of GDMR in sheep. The experiment was conducted on 1,047 Romane sheep allocated into 10 half-sib families. After weaning, all the lambs were phenotyped for global GDMR in blood as well as for production and adaptive traits. GDMR was measured by LUminometric Methylation Analysis (LUMA) using a pyrosequencing approach. Association analyses were conducted on some of the lambs (n = 775) genotyped by using the Illumina OvineSNP50 BeadChip. Blood GDMR varied among the animals (average 70.7 ± 6.0%). Female lambs had significantly higher GDMR than male lambs. Inter-individual variability of blood GDMR had an additive genetic component and heritability was moderate (h2 = 0.20 ± 0.05). No significant genetic correlation was found between GDMR and growth or carcass traits, birthcoat, or social behaviors. Association analyses revealed 28 QTLs associated with blood GDMR. Seven genomic regions on chromosomes 1, 5, 11, 17, 24, and 26 were of most interest due to either high significant associations with GDMR or to the relevance of genes located close to the QTLs. QTL effects were moderate. Genomic regions associated with GDMR harbored several genes not yet described as being involved in DNA methylation, but some are already known to play an active role in gene expression. In addition, some candidate genes, CHD1, NCO3A, KDM8, KAT7, and KAT6A have previously been described to be involved in epigenetic modifications. In conclusion, the results of the present study indicate that blood GDMR in domestic sheep is under polygenic influence and provide new insights into DNA methylation genetic determinism.

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Section: Discussionmentioning

confidence: 99%

Genetic Determinism Exists for the Global DNA Methylation Rate in Sheep

et al. 2020

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“…Pearson correlation analysis was used to evaluate the relationship between NFE2L2 expression and MMR gene mutation levels. In addition, DNA methyltransferases play an important role in altering chromatin structure and gene expression [ 23 ]. The relationship between the expression level of NFE2L2 and that of 4 methyltransferases (DNMT1, DNMT2, DNMT3A, and DNMT3B) was evaluated by Pearson correlation analysis.…”

Section: Methodsmentioning

confidence: 99%

NFE2L2 Is a Potential Prognostic Biomarker and Is Correlated with Immune Infiltration in Brain Lower Grade Glioma: A Pan-Cancer Analysis

Zhang

et al. 2020

Oxidative Medicine and Cellular Longevity

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Nuclear factor, erythroid 2 like 2 (NFE2L2, NRF2) is a transcription factor that regulates various antioxidant enzymes. It plays a vital physiological role in regulating oxidative stress and inflammatory response. However, the roles of NFE2L2 in human cancers are still unclear. Our study is aimed at analyzing the prognostic value of NFE2L2 in pan-cancer and at revealing the relationship between NFE2L2 expression and tumor immunity. The present study revealed that NFE2L2 was abnormally expressed and significantly correlated with mismatch repair (MMR) gene mutation levels and DNA methyltransferase expression in human pan-cancer. In particular, pan-cancer survival analysis indicated that NFE2L2 expression was associated with adverse outcomes—overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI)—in adrenocortical carcinoma (ACC), brain lower grade glioma (LGG), and pancreatic adenocarcinoma (PAAD) patients. A positive relationship was also found between NFE2L2 expression and immune infiltration, including B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells, especially in breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), kidney renal clear cell carcinoma (KIRC), LGG, liver hepatocellular carcinoma (LIHC), and prostate adenocarcinoma (PRAD). Additionally, NFE2L2 expression was positively correlated with the immune score and the expression of immune checkpoint markers in LGG. In conclusion, these results indicate that transcription factor NFE2L2 is a potential prognostic biomarker and is correlated with immune infiltration in LGG.

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“…Specific epi-signatures have been recently demonstrated in other CRDs, including Genitopatellar and Say-Barber-Biesecker-Young-Simpson syndromes, Werner syndrome, Williams and 7q11.23 duplication syndromes, progressive supranuclear palsy and frontotemporal dementia, Cornelia de Lange and SETD1B-related syndromes [15,29,44,45]. Details on the aetiology and methylation patterns of these disorders are reported in Table 1.…”

Section: Chromatin-related Disordersmentioning

confidence: 95%

DNA Methylation in the Diagnosis of Monogenic Diseases

Cerrato

Sparago

Ariani

et al. 2020

Genes

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DNA methylation in the human genome is largely programmed and shaped by transcription factor binding and interaction between DNA methyltransferases and histone marks during gamete and embryo development. Normal methylation profiles can be modified at single or multiple loci, more frequently as consequences of genetic variants acting in cis or in trans, or in some cases stochastically or through interaction with environmental factors. For many developmental disorders, specific methylation patterns or signatures can be detected in blood DNA. The recent use of high-throughput assays investigating the whole genome has largely increased the number of diseases for which DNA methylation analysis provides information for their diagnosis. Here, we review the methylation abnormalities that have been associated with mono/oligogenic diseases, their relationship with genotype and phenotype and relevance for diagnosis, as well as the limitations in their use and interpretation of results.

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A genome-wide DNA methylation signature for SETD1B-related syndrome

Cited by 51 publications

References 32 publications

Genetic Determinism Exists for the Global DNA Methylation Rate in Sheep

Genetic Determinism Exists for the Global DNA Methylation Rate in Sheep

NFE2L2 Is a Potential Prognostic Biomarker and Is Correlated with Immune Infiltration in Brain Lower Grade Glioma: A Pan-Cancer Analysis

DNA Methylation in the Diagnosis of Monogenic Diseases

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